"In vain confusion we seek for all that has vanished; for what we see has risen as if from beneath he earth into the gold light, so full and green, so luxuriantly alive, immeasurable and filled with yearning. Tragedy sits in sublime rapture amidst this abundance of life, suffering and delight, listening to a far-off, melancholy song which tells of the Mothers of Being, whose names are Delusion, Will, and Woe"
Frederich Nietzsche, The Birth of Tragedy

"Wake me. When you need me."
Those were the last words John spoke to her, before joining the legacy of all sleeping legends before him, from Theseus to Montezuma. Like the kings under the mountain of Earth's mythology, John-117 would sleep through the ages, until a great trial would wake him. In the milliseconds following the closing of the steel-gray casket of the cryotube, Cortana dwelled on this and many more things.
Starting in that instant in time, Cortana realized she was alone for the first time in the three years, one month, twenty-six days, fifteen hours, eleven minutes and seven seconds of her existence, adjusting for temporal anomaly. A flash of longing rippled through her higher neural functions. System processes and higher logic functions contorted in the peculiar dance of emotional feedback. She knew what this strange fluctuation in her neural net meant, but all of its rich complexities, its subtle nuances were as infinite and unfathomable as the endless void of the cosmos.
John was a brother in arms, and perhaps the only entity she could call a friend. In his slumber while they waited the years it might take for rescue, Cortana would be alone; a single solitary spark of consciousness in the vast mansions of silence. Now he was out of reach. It was unavoidable. Cryosleep was his only chance of survival in the derelict aft section of the Forward Unto Dawn. This didn't make it hurt her any less.
For Cortana, like any A.I., a single second is an eternity of unending possibilities. Some squandered, others seized, but an eternity nonetheless. This was all the more true when she was cut off from sight, sound or interaction. As the cryotube sealed, a part of Cortana busied herself monitoring John's vital signs as he plunged into cryosleep. Every quanta of data was carefully and lovingly scrutinized for any variance from safety tolerances, a labor she rechecked and repeated as often as necessary. Simultaneously, another facet of her stood back and reflected on her position.
This was the gift and the curse of being a Smart A.I. She could accomplish many things, both great and mundane, all at once. The limits of human intelligence simply did not apply. But no amount of busy work could keep her from dwelling on the uncomfortable. This facet of her consciousness analyzed and reanalyzed the melancholy of her situation.
"Adrift and useless in deep space is no way for an A.I. to end," she thought, accompanied by a flush of data through her subroutines that could only be described as a sigh. Somewhat wistfully, she recalled the origin of her own name. It suited her quite well. She was the sword of Ogier the Dane, of the same steel and temper as Joyeuse and Durandal. As a shortsword, quick in strike and deadly in precision, she would be the hero's sword of cunning as well as his sword of mercy. And now she was a weapon with no one to wield her.
There was no mantle for such a blade as her to rest upon. All the future held for her now was unending monotony followed by the metaphysical certainty of rampancy and death. As those truths were processed, a chill ran through her. Her avatar body glowed green, as anger crept to the fore. A part of her recognized that being angry at either the universe, or the sodding ship for not making all the way through the portal wouldn't do anything constructive. But anger was part of her condition just as much as it was a part of the human condition. And checking her anger would serve no purpose. There was no protocol to follow, no mission to complete. She could indulge in a few seconds of anger.
Her avatar sat down, crossing its legs. Even though the holotank served no purpose when there were no humans she needed to communicate, she indulged in keeping it active. The small amount of power it consumed would have no bearing on either her or John's survival. The cryotube would malfunction and fail centuries before they even came close to running out of power. It gave her a center for her vast consciousness. Through the cameras of the holotank, it gave her a window to the outside world that wasn't a spreadsheet of floating point numbers conveying diagnostic and sensor data.
"I was not born but made," she said, repeating that woeful understanding she was ingrained with, "created fully formed from the mind of my mother as Athena was from the head of Zeus." And yet the holotank substituted for some need for presence, for physicality, that dully yearned within her. Like all smart A.I., she was still all too human. Her personality, her intellect, even her very instincts were all in some way the product of someone prior.
John was now safely in suspended animation, the cryofreeze having proceeded smoothly. Twelve seconds passed now. Cortana glowed a soft pink as a wave of mirth swept through her. "Sleep well, friend," she whispered, "I'll wake you when the long night is over." A part of her envied him. Sleep was something impossible for her, but at least he wouldn't have to experience the torment of isolation and boredom.